In the file CryptA.bol I found entries for the two Jindols:
Offset 1,600, I077, [Item 77, Warrior's Jindol], 0, 3, 107, 71, 0, 64, 63, 68, 0, 198, 222, 70
Offset 1,664, I078, [Item 78, Wizard's Jindol], 0, 3, 107, 71, 0, 64, 63, 68, 0, 232, 172, 197
Both Jindols would seem to have about the same X and Z coordinates, where Z is the height. They should differ mainly in the Y coordinate. Entries differ in the fourth offset and in the last three, hence the last three are probably the Y coordinate.

In the second room inside the Crypt there is a skull lying on a table. Adding +1 to the 198 made the skull disappear, presumably its position was shifted well south of the relevant room. Adding +18 to the 237 moved it a few feet south of the table. Y coordinate would seem to be 112, 59, 237, 198.
Offset 29,504, I251, [Item 251, Skull], 40, 22, 45, 199, 0, 160, 53, 69, 112, 59, 237, 198

Going from the right of each four byte group, adding 1 to the second number moves the item very roughly 6" in apparent terms. Thus changing the 45 to a 50 moved the skull a few feet. (Left not right too.)
40, 22, 45, 199,
0, 160, 53, 69,
112, 59, 237, 198

With understanding of coordinates it is possible to figure out where to place a new item, what coordinates to use.
I may be able to pin down which chest is which, something I can't currently do.

I can spot the three Receptacle Locks and the two Vestal urns in the Bol file, I just can't see what makes them work. It might be possible for me to find a file where the five known item numbers all occur.

D6Swit01.dat:
Numbering columns from 0 to 19, columns 12 and 13 seem to contain the numbers of the activating items.
I can't conclusively link the entries in this file to the entries in the bol file...

CryptA.bol: Algamesh's Amulet is found in the second, in the chest near the Skull.
Prop 1, offset 128, "P006" = Treasure Chest
CryptB.bol: Bauble Stick is found in the chest in the room to the south east of Rethpian.
Prop 11, offset 768, "P006" = Treasure Chest
I was able to verify the two guesses by replacing the chests with various items.
What I don't get is how they are assigned the treasure types listed in D6Trap01.dat?

I was trying to move the Serpent Idol in the Serpent Holds, of the Serpent Temple, to a more accessible place. I wanted the coordinates of the center of one of the two pools. Hence I placed some items on the ground and then saved the game. When I examined the save game file I was able to find the items in the file, I just could not find the coordinates that I expected. So items lying on the ground have their own coordinate system or I have yet to find the coordinates.

(Accessing this idol is no problem whatsoever, if you have the Vanish spell handy.)

Using the coordinates of
(1) the current location of the Serpent Idol
(2) the Unholy Filth monster
(3) the Skull lock
I was able to figure out new coordinates for the Serpent Idol that put it in the right hand pool, underwater.
Here are the coordinates in Assembler data format:
data db 49h,31h,31h,33h,40h,00h,30h,C7h,00h,DDh,CDh,C6h,00 h,FCh,D7h,45h

One way to obtain the coordinates of a point is to interpolate from known positions of existing objects. Cast Spirit Eye so all usable objects show up, then make a screenshot of the area map.
When looking at a screenshot of the Serpent Holds area, I figured out that to increase the distance to the left by N in pixels, required an increase of 3/5 of N in the second digit in the X coordinate in the Bol file.

I don't know how to describe the Zoom level that I had at the time. One approach, the area explored was one-quarter of the total map screen area.

Bsftc's maps may not always be useful here. He made various improvements to try and give the big picture, get around the Salami slices nature of the automaps.
Best idea is to use your own screenshots, with all of them set to the same level of Zoom in/Zoom out.
A freeware program like Greenshot can enable you to take as many screenshots as you like. (Some of the shots may lead to the game display flickering badly... Shut down the automap if that happens, then restart it.)